It takes more than 24 hours to resync most of the time. This is not something anyone here can help you with. All we can do is state what we did, how it happened to us and what not.

Contacting Gamefreak and TPC or Nintendo will give you a generic message.

Your game cannot be played for the duration of the 24 hours iirc. If it still does not fix after that try contacting TPC or Nintendo with your issue, in a respectible manner. No ALL CAPS AND EXCLAMATIONS EVERYWHERE!!!!!!!!!!!!!!!!!!!!!!!!

If a person were to see that in their inbox when looking over their technical difficulties reviews they will close your issue and completely ignore you.

The only thing you can do is wait it out. It will sync eventually so long as they don't shut down the site.